[gmx-users] bilayer area questions WITH DATA

[David]

On Wed, 2005-09-14 at 11:23 -0700, Rama Gullapalli wrote:
> Dear David
> Thanks for the reply. Maybe im not getting this
> straight, But this was the inital box volume too,
> since i have scaled the value of the vectors of the
> box to be this at the beginning of the simulation.
> 
> Putting it another way, does the size of the system
> have NOTHING to do with the box size and as a result,
> the area per lipid ?....
size of the system is quite meaningless as it includes molecules
sticking out of the box which can be a lot with lipids.
> 
> I did plot the value of the length of the box x vs
> time and length of box y vs time and as i expected it
> is hovering around the values of the initial values of
> the box. 
> 
> But the system is 7.8 by 8.1 so isnt the area per
> lipid equal to 7.8 *8.1/ 64 for a 128 lipid system?
> 
> or is it still 5.6 * 5.8 / 64?
Yes.

> 
> Im quite throughly confused.
> Thanks for your time and patience :)
> Regards
> Rama
> 
> 
> --- David <spoel at xray.bmc.uu.se> wrote:
> 
> > On Wed, 2005-09-14 at 09:12 -0700, Rama Gullapalli
> > wrote:
> > > Dear Dr Warren
> > > Thank you for your replies. Here is the data which
> > i
> > > got for the whole equilibriation process which is
> > > causing me the confusion.
> > > 
> > > 1) After 100 picoseconds of equilibriation
> > > new system size :  6.346  6.414  8.734
> > > new center      :  2.949  2.909  4.294 (nm)
> > > new box vectors :  5.847  5.762  8.600 (nm)
> > > new box angles  :  90.00  90.00  90.00 (degrees)
> > > new box volume  : 289.74               (nm^3)
> > > 
> > > 2) After 2 nanoseconds of equilibriation
> > > 
> > > new system size :  8.032  7.517  8.685
> > > new center      :  2.866  2.906  4.259 (nm)
> > > new box vectors :  5.736  5.915  8.539 (nm)
> > > new box angles  :  90.00  90.00  90.00 (degrees)
> > > new box volume  : 289.69               (nm^3)
> > > 
> > > 3) After 10 nanoseconds of equilbriation
> > > 
> > > new system size :  7.368  8.177  8.785
> > > new center      :  2.881  2.936  4.316 (nm)
> > > new box vectors :  5.692  5.876  8.640 (nm)
> > > new box angles  :  90.00  90.00  90.00 (degrees)
> > > new box volume  : 288.95               (nm^3)
> > > 
> > > As you can see, the box size has remained
> > constant,
> > > but the system size has increased progressively
> > and
> > > the seems to begin to decrease too.
> > > 
> > > So my question is do i need to keep equilibriating
> > the
> > > system till it reaches the original size or is
> > there
> > > something i can do right at the outset(like
> > specify
> > > the density in editconf) so that the system does
> > not
> > > expand.
> > > 
> > > Also, why do the box vector sizes do not increase?
> > The volume is constant and the box vectors have
> > stabilized. Plot the box
> > vectors as a function of time to check equilibration
> > (using g_energy)
> > 
> > 
> > -- 
> > David.
> >
> ________________________________________________________________________
> > David van der Spoel, PhD, Assoc. Prof., Molecular
> > Biophysics group,
> > Dept. of Cell and Molecular Biology, Uppsala
> > University.
> > Husargatan 3, Box 596,          75124 Uppsala,
> > Sweden
> > phone:  46 18 471 4205          fax: 46 18 511 755
> > spoel at xray.bmc.uu.se    spoel at gromacs.org  
> > http://xray.bmc.uu.se/~spoel
> >
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> 
> 
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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